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9qmt

Arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase in complex with Mesotrione (Mn)

Method: X-RAY DIFFRACTION D_max: 75.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qmt
deposition_date	2025-03-24
last_revision	2026-04-08
title	Arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase in complex with Mesotrione (Mn)
keywords	;Dioxygenase, Phenylalanine catabolism, Tyrosine catabolism, Iron, Metal-binding, 4-hydroxyphenylpyruvate, homogentisic acid, OXIDOREDUCTASE ;; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	21.80 Å
rg_electron	20.61 Å
i0	29726200.00
molecular_weight	41943.0 kDa
excluded_volume	52468 Å³
envelope_volume	60429 Å³
shell_volume	24071 Å³
envelope_diameter	71.7 Å
shell_rg	27.85 Å
envelope_rg	20.95 Å
shape_rg	20.59 Å
total_rg	21.56 Å
total_atoms	2953
n_residues	376
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	75.1 Å
rg_real	21.69 Å
rg_real_error	0.47 Å
i0_real	2.9730e+07
i0_real_error	3.9510e+05
rg_reciprocal	21.71 Å
i0_reciprocal	29730000.0000
total_estimate	0.8592
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	28.0 Å
skewness	0.239
kurtosis	-0.232
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	6142000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.725; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	4-hydroxyphenylpyruvate dioxygenase
formula_weight	45343.0 kDa
ec_number	1.13.11.27
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3105

GGSVRKNPKSDKFKVKRFHHIEFWCGDATNVARRFSWGLGMRFSAKSDLSTGNMVHASYLLTSGDLRFLFTAPYSPSLSAGEIKPTTTASIPSFDHGSCRSFFSSHGLGVRAVAIEVEDAESAFSISVANGAIPSSPPIVLNEAVTIAEVKLYGDVVLRYVSYKAEDTEKSEFLPGFERVEDASSFPLDYGIRRLDHAVGNVPELGPALTYVAGFTGFHQFAEFTADDVGTAESGLNSAVLASNDEMVLLPINEPVHGTKRKSQIQTYLEHNEGAGLQHLALMSEDIFRTLREMRKRSSIGGFDFMPSPPPTYYQNLKKRVGDVLSDDQIKECEELGILVDRDDQGTLLQIFTKPLGDRPTIFIEIIQRVGCMMKDEEGKAYQSGGCGGFGKGNFSELFKSIEEYEKTLEAK

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	2-[(4-methylsulfonyl-2-nitro-phenyl)-oxidanyl-methylidene]cyclohexane-1,3-dione
formula_weight	339.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	131

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6. Citations (1)

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length_a	76.635 Å
length_b	83.628 Å
length_c	61.530 Å
angle_alpha	90.00 °
angle_beta	100.64 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.000 Å
resolution_low	34.390 Å
r_factor	0.1882
r_work	0.1868
r_free	0.2148

fit	/app/data/saxs_computation/qm/9qmt/9qmt.fit
pddf	/app/data/pr_computation/qm/9qmt/9qmt.pr.out
profile	/app/data/saxs_computation/qm/9qmt/9qmt.dat